ID code: '2OJ7' CHIRALITY (03 Nov 1998) Checks the chirality and the naming of substituents of chiral and prochiral centers in nucleic acid structures. The molecular structure is read from a PDB file. Only the first model is evaluated. ---------------------------------------------------------- Center Reference for correct naming ---------------------------------------------------------- C1' alpha/beta nomenclature of anomeric sugars, base in beta position in natural nucleosids. C2' IUPAC. 1983. Eur J Biochem, 131: 9-15. C3' IUPAC. 1983. Eur J Biochem, 131: 9-15. C4' IUPAC. 1983. Eur J Biochem, 131: 9-15. C5' IUPAC. 1983. Eur J Biochem, 131: 9-15. P Brookhaven PDB entry '1BNA', O1P -> major groove, O2P -> minor groove. ---------------------------------------------------------- Author: Peter Slickers (slickers@imb-jena.de) Biocomputing, IMB Jena, Germany --------------------------------------------------------------------------------- Seq No Atom Residue H1' base O4' H1' base C2' --------------------------------------------------------------------------------- 12 C1' G A 11 alpha beta 7 30 13 10 46 C1' C A 12 alpha beta 41 61 47 44 77 C1' U A 13 alpha beta 72 92 78 75 107 C1' G A 14 alpha beta 102 125 108 105 141 C1' U A 15 alpha beta 136 156 142 139 171 C1' U A 16 alpha beta 166 186 172 169 201 C1' G A 17 alpha beta 196 219 202 199 235 C1' U A 18 alpha beta 230 250 236 233 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G A 11 OK OK 12 8 28 11 44 C2' C A 12 OK OK 46 42 59 45 75 C2' U A 13 OK OK 77 73 90 76 105 C2' G A 14 OK OK 107 103 123 106 139 C2' U A 15 OK OK 141 137 154 140 169 C2' U A 16 OK OK 171 167 184 170 199 C2' G A 17 OK OK 201 197 217 200 233 C2' U A 18 OK OK 235 231 248 234 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G A 11 OK OK 6 27 9 10 42 C3' C A 12 OK OK 40 58 43 44 73 C3' U A 13 OK OK 71 89 74 75 103 C3' G A 14 OK OK 101 122 104 105 137 C3' U A 15 OK OK 135 153 138 139 167 C3' U A 16 OK OK 165 183 168 169 197 C3' G A 17 OK OK 195 216 198 199 231 C3' U A 18 OK OK 229 247 232 233 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G A 11 OK OK 8 26 5 7 40 C4' C A 12 OK OK 42 57 39 41 71 C4' U A 13 OK OK 73 88 70 72 101 C4' G A 14 OK OK 103 121 100 102 135 C4' U A 15 OK OK 137 152 134 136 165 C4' U A 16 OK OK 167 182 164 166 195 C4' G A 17 OK OK 197 215 194 196 229 C4' U A 18 OK OK 231 246 228 230 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G A 11 OK OK 4 24 25 6 39 C5' C A 12 OK OK 38 55 56 40 70 C5' U A 13 OK OK 69 86 87 71 100 C5' G A 14 OK OK 99 119 120 101 134 C5' U A 15 OK OK 133 150 151 135 164 C5' U A 16 OK OK 163 180 181 165 194 C5' G A 17 OK OK 193 213 214 195 228 C5' U A 18 OK OK 227 244 245 229 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G A 11 distorted distorted 2 3 4 35 P C A 12 distorted distorted 9 36 37 38 66 P U A 13 distorted distorted 43 67 68 69 96 P G A 14 distorted distorted 74 97 98 99 130 P U A 15 distorted distorted 104 131 132 133 160 P U A 16 distorted distorted 138 161 162 163 190 P G A 17 distorted distorted 168 191 192 193 224 P U A 18 distorted distorted 198 225 226 227 ---------------------------------------------------------------------------------